Apps missing after Root

Apps missing after Root

I looked and didn't see a tread for this so, I just rooted my Bionic and then downloaded and installed AdFree and went to check it on some of the apps I have downloaded, so I click on one of them from my home screen and it says app not downloaded. I look in my app draw it there are a few apps missing. Has anyone else ran into this? Is this normal? This is the first phone I've rooted. But AdFree did work on the apps that didn't get deleted. Thanks